Align dihydroxyacid dehydratase (characterized)
to candidate PfGW456L13_973 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= CharProtDB::CH_024768
(616 letters)
>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973
Length = 613
Score = 912 bits (2358), Expect = 0.0
Identities = 458/617 (74%), Positives = 519/617 (84%), Gaps = 6/617 (0%)
Query: 1 MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
MP YRS T+THGRNMAGARALWRATGM D DF KPIIA+ NSFTQFVPGHVHL+DLG+LV
Sbjct: 1 MPDYRSKTSTHGRNMAGARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLV 60
Query: 61 AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
A +IE AGGVAKEFNTIAVDDGIAMGH GMLYSLPSRE+IADSVEYMVNAHCADA+VCIS
Sbjct: 61 AREIERAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 120
Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKL+ LDLVDAM+ AD SD +
Sbjct: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLASH--GLDLVDAMVIAADSSASDEK 178
Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
+ ERSACPTCGSCSGMFTANSMNCL EALGL+ PGNGS LATH+DR+QLFL AG+ IV
Sbjct: 179 VAEYERSACPTCGSCSGMFTANSMNCLVEALGLALPGNGSTLATHSDREQLFLQAGRTIV 238
Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
EL KRYY +ND+S LPRNIA+ AFENAMTLDIAMGGSTNT+LHLLAAAQEAEIDF + D
Sbjct: 239 ELCKRYYGENDQSVLPRNIANFQAFENAMTLDIAMGGSTNTILHLLAAAQEAEIDFDLRD 298
Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT 360
ID+LSR VPQLCKVAP+ QKYHMEDVHRAGG+ ILG L R GLL+ + V ++ +
Sbjct: 299 IDRLSRNVPQLCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTQLPTVHSRSMEEA 358
Query: 361 LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG 420
+ ++D+ T D+AV + F+AGPAGI T AFSQ RW+TLDDDR NGCIRS+EHAYS++G
Sbjct: 359 IAKWDITQTNDEAVHHFFKAGPAGIPTQTAFSQSTRWETLDDDRENGCIRSVEHAYSQEG 418
Query: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY 480
GLAVLYGN A +GC+VKTAGVD+SI F G AK++ESQD AV IL +V GD+V+IRY
Sbjct: 419 GLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGILADEVKEGDIVIIRY 478
Query: 481 EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL 540
EGPKGGPGMQEMLYPTS+LKS GLGKACAL+TDGRFSGGTSGLSIGH SPEAA+GG+IGL
Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGL 538
Query: 541 IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTP-KNRERQVSFALRAYASL 599
++DGD + IDIPNR I L VSD ELAARR QD +G W P + R R+V+ AL+AYA L
Sbjct: 539 VQDGDKVLIDIPNRSINLLVSDEELAARRVEQDKKG---WKPVEVRPRKVTTALKAYALL 595
Query: 600 ATSADKGAVRDKSKLGG 616
ATSADKGAVR+K+ L G
Sbjct: 596 ATSADKGAVRNKAMLDG 612
Lambda K H
0.317 0.134 0.386
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1216
Number of extensions: 43
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 616
Length of database: 613
Length adjustment: 37
Effective length of query: 579
Effective length of database: 576
Effective search space: 333504
Effective search space used: 333504
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)
Align candidate PfGW456L13_973 (Dihydroxy-acid dehydratase (EC 4.2.1.9))
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.aa/TIGR00110.hmm
# target sequence database: /tmp/gapView.1089.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00110 [M=543]
Accession: TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
9.7e-255 832.1 1.2 1.1e-254 831.9 1.2 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 Dihydroxy-acid dehydratase (EC 4
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 Dihydroxy-acid dehydratase (EC 4.2.1.9)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 831.9 1.2 1.1e-254 1.1e-254 2 542 .. 18 606 .. 17 607 .. 0.98
Alignments for each domain:
== domain 1 score: 831.9 bits; conditional E-value: 1.1e-254
TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvake 57
aral++atG+kd+d++kPiia++ns+t++vPghvhlkdl++lv++eie+aGgvake
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 18 ARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKE 73
79****************************************************** PP
TIGR00110 58 fntiavsDGiamgheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGm 113
fntiav+DGiamgh+Gm+ysLpsreiiaDsve++v+ah++Da+v+is+CDki+PGm
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 74 FNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCISNCDKITPGM 129
******************************************************** PP
TIGR00110 114 lmaalrlniPaivvsGGpmeagktklsekidlvdvfeavgeyaagklseeeleeie 169
lma+lrlniP+i+vsGGpmeagktkl + +d+++a++ +a++ s+e++ e+e
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 130 LMASLRLNIPVIFVSGGPMEAGKTKL--ASHGLDLVDAMVIAADSSASDEKVAEYE 183
*************************8..557899********************** PP
TIGR00110 170 rsacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkrive 225
rsacPt+gsCsG+ftansm+cl ealGl+lPg++++lat++++++l+ ++g++ive
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 184 RSACPTCGSCSGMFTANSMNCLVEALGLALPGNGSTLATHSDREQLFLQAGRTIVE 239
******************************************************** PP
TIGR00110 226 lvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvkls 274
l+k+++ Pr+i++ +afena+tld+a+GGstnt+Lhlla+a+ea+++++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 240 LCKRYYGendqsvlPRNIANFQAFENAMTLDIAMGGSTNTILHLLAAAQEAEIDFD 295
*****999999********************************************* PP
TIGR00110 275 lddfdrlsrkvPllaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvt 329
l d+drlsr+vP+l+k++P+ +k+ +ed+hraGG+ ++l++l + gllh++ tv
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 296 LRDIDRLSRNVPQLCKVAPNIQKYhMEDVHRAGGIFSILGSLARGGLLHTQLPTVH 351
*********************9999******************************* PP
TIGR00110 330 Gktlaetlekvkvlr...................................vdqdvi 350
++++e ++k ++++ ++ +i
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 352 SRSMEEAIAKWDITQtndeavhhffkagpagiptqtafsqstrwetldddRENGCI 407
*************999******************************77555555** PP
TIGR00110 351 rsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeai 406
rs+++++++egglavL+Gn+a +G+vvk+agv+e+i +feG+ak+fes++ a+ +i
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 408 RSVEHAYSQEGGLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGI 463
******************************************************** PP
TIGR00110 407 lggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtr 462
l+ +vkeGd+v+iryeGPkGgPGm+emL+Pts+l++ GLgk++aL+tDGrfsGgt+
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 464 LADEVKEGDIVIIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTS 519
******************************************************** PP
TIGR00110 463 GlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea 518
GlsiGh sPeaa+gGai+lv+dGDk+ iDi+nr ++l vs+eela+rr +++kk++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 520 GLSIGHASPEAAAGGAIGLVQDGDKVLIDIPNRSINLLVSDEELAARRVEQDKKGW 575
******************************************************** PP
TIGR00110 519 .......revkgaLakyaklvssadkGavld 542
r+v aL++ya l++sadkGav++
lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 576 kpvevrpRKVTTALKAYALLATSADKGAVRN 606
9****9999********************87 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (543 nodes)
Target sequences: 1 (613 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.89
//
[ok]
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory